Variant report

Variant	rs5997949
Chromosome Location	chr22:31701821-31701822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1034588	0.80[EUR][1000 genomes]
rs12152166	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13054220	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs131205	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1858821	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2040533	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2073857	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2078803	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2106294	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2228619	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2283879	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2283881	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2413046	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2413047	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2413049	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4141404	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4603880	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4820043	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4820962	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4820963	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753521	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753543	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5997933	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5997939	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71324184	0.85[EUR][1000 genomes]
rs714909	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs715510	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7287267	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737684	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs737887	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737888	0.80[EUR][1000 genomes]
rs8135344	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8138596	0.83[EUR][1000 genomes]
rs9606830	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9606831	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9609254	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9609257	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9609264	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9609265	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9609266	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9609267	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9609268	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9621235	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5997949	SFI1	cis	Thyroid	GTEx
rs5997949	DRG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31689400-31709000	Weak transcription	Placenta	Placenta
2	chr22:31690200-31704200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr22:31692600-31709200	Weak transcription	Stomach Mucosa	stomach
4	chr22:31693400-31702400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr22:31693400-31709200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr22:31693800-31720000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr22:31694200-31702600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr22:31695000-31703000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr22:31697000-31709400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr22:31697400-31702600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr22:31697400-31704800	Weak transcription	Small Intestine	intestine
12	chr22:31697800-31702600	Weak transcription	HepG2	liver
13	chr22:31698000-31709200	Weak transcription	Adipose Nuclei	Adipose
14	chr22:31698400-31702400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr22:31698400-31709200	Weak transcription	Fetal Intestine Small	intestine
16	chr22:31698600-31702200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr22:31698600-31702400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr22:31698600-31702400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr22:31698800-31702000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr22:31698800-31702400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr22:31699000-31702200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr22:31699200-31702400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr22:31700600-31703000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr22:31700800-31702400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr22:31700800-31702400	Enhancers	NHEK	skin
26	chr22:31700800-31703000	Enhancers	HMEC	breast
27	chr22:31701200-31704000	Weak transcription	Primary T cells from cord blood	blood
28	chr22:31701400-31702400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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